The invention provides a method of determining a comparative expression profile in an individual by comparing the expression levels of a sample of molecules in a population of molecules in a specimen from the individual with a health-associated reference expression region of the sample of molecules, wherein expression levels within the health-associated reference expression region indicate a reference expression profile and wherein expression levels outside the health-associated reference expression region indicate a perturbed expression profile. The invention also provides methods of diagnosing a disease or a health state in an individual by comparing the expression level of a sample of molecules in a specimen from the individual with a health-associated reference expression region of the sample of molecules. The invention additionally provides a method of classifying a population by drug responsiveness.
Legal claims defining the scope of protection, as filed with the USPTO.
1. A computational method of classifying a population by drug responsiveness, comprising: (a) creating a multidimensional space of n dimensions, wherein n represents the number of different molecules being analyzed in a specimen from each individual in a population of individuals administered a drug and wherein said multidimensional space contains n axes, each of said axes relating to the expression level of a molecule of said n molecules, wherein n is 3 or more molecules and wherein said molecules are nucleic acids or polypeptides; (b) determining multidimensional coordinate points for each individual in said population, wherein each of said multidimensional coordinate points is representative of the expression levels of said n molecules in each of said individuals; (c) determining a drug response-associated reference expression region of a group of individuals in said population using said multidimensional coordinate points, thereby classifying said group of individuals into a drug response reference population; and (d) providing an output of said classification of said drug response reference population to a user.
2. The method of claim 1 , further comprising the step of correlating said group of individuals with a response to said drug.
3. The method of claim 2 , wherein said response is alleviation of a sign or symptom associated with a condition of an individual administered said drug.
4. The method of claim 1 , wherein the expression levels of said molecules are determined by contacting said specimen with a target.
5. The method of claim 4 , wherein said target is an array.
6. The method of claim 4 , wherein said target comprises nucleic acid ligands.
7. The method of claim 4 , wherein said target comprises antibody ligands.
8. The method of claim 1 , wherein said specimen is selected from the group consisting of leukocytes, blood, and serum.
9. The method of claim 1 , wherein said molecules in said specimen comprise nucleic acids.
10. The method of claim 1 , wherein said molecules in said specimen comprise polypeptides.
11. The method of claim 1 , wherein n is 5 or more molecules.
12. The method of claim 1 , wherein n is 10 or more molecules.
13. The method of claim 1 , wherein n is 20 or more molecules.
14. The method of claim 1 , wherein n is 50 or more molecules.
15. The method of claim 1 , wherein n is 100 or more molecules.
16. The method of claim 1 , wherein n is 200 or more molecules.
17. The method of claim 1 , wherein n is 500 or more molecules.
18. The method of claim 1 , wherein n is 1000 or more molecules.
19. A computational method of classifying a population by drug responsiveness, comprising: (a) creating a multidimensional space of n dimensions, wherein n represents the number of different molecules being analyzed in a specimen comprising leukocytes from each individual in a population of individuals administered a drug and wherein said multidimensional space contains n axes, each of said axes relating to the expression level of a molecule of said n molecules,wherein n is 3 or more molecules and wherein said molecules are nucleic acids or polypeptides; (b) determining multidimensional coordinate points for each individual in said population, wherein each of said multidimensional coordinate points is representative of the expression levels of said n molecules in each of said individuals; (c) determining a drug response-associated reference expression region of a group of individuals in said population using said multidimensional coordinate points, thereby classifying said group of individuals into a drug response reference population; and d) providing an output of said classification of said drug response reference population to a user.
20. The method of claim 19 , further comprising the step of correlating said group of individuals with a response to said drug.
21. The method of claim 20 , wherein said response is alleviation of a sign or symptom associated with a condition of an individual administered said drug.
22. The method of claim 19 , wherein the expression levels of said molecules are determined by contacting said specimen with a target.
23. The method of claim 22 , wherein said target is an array.
24. The method of claim 22 , wherein said target comprises nucleic acid ligands.
25. The method of claim 22 , wherein said target comprises antibody ligands.
26. The method of claim 19 , wherein said molecules in said specimen comprise nucleic acids.
27. The method of claim 19 , wherein said molecules in said specimen comprise polypeptides.
28. The method of claim 19 , wherein n is 5 or more molecules.
29. The method of claim 19 , wherein n is 10 or more molecules.
30. The method of claim 19 , wherein n is 20 or more molecules.
31. The method of claim 19 , wherein n is 50 or more molecules.
32. The method of claim 19 , wherein n is 100 or more molecules.
33. The method of claim 19 , wherein n is 200 or more molecules.
34. The method of claim 19 , wherein n is 500 or more molecules.
35. The method of claim 19 , wherein n is 1000 or more molecules.
Cooperative Patent Classification codes for this invention. Click any code to explore related patents in that topic.
July 30, 2001
March 11, 2008
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